Hi Maintainer

The SyntaxWarning below were emitted when this package was tested with
pipuarts[1].

Regards
Graham


[1] https://piuparts.debian.org/sid/source/p/python-csb.html


  Setting up python3-csb (1.2.5+dfsg-10) ...
  /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:210:
SyntaxWarning: invalid escape sequence '\d'
    m = re.search('(\d+)\D+(\d+)', line).groups()
  /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:260:
SyntaxWarning: invalid escape sequence '\s'
    seq = re.sub('\s+', '', ''.join(lines[1:]))
  /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:307:
SyntaxWarning: invalid escape sequence '\-'
    pattern = re.compile('^[A-Z\-]\s[0-9]+\s+')
  /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:31:
SyntaxWarning: invalid escape sequence '\s'
    input_file_name = re.compile('>>>-----.*?\n.*?\n\s*\|\s*(\S+)\s+')
  /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:32:
SyntaxWarning: invalid escape sequence '\d'
    residues = re.compile('(\d+)\s*residues\s\|')
  /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:33:
SyntaxWarning: invalid escape sequence '\s'
    ramachandran_plot = re.compile('Ramachandran\splot:\s*(\d+\.\d+)' +
  /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:34:
SyntaxWarning: invalid escape sequence '\s'
    '%\s*core\s*(\d+\.\d+)%\s*allow\s*(\d+\.\d+)' +
  /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:35:
SyntaxWarning: invalid escape sequence '\s'
    '%\s*gener\s*(\d+\.\d+)%\s*disall')
  /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:36:
SyntaxWarning: invalid escape sequence '\s'
    labelled_all = re.compile('Ramachandrans:\s*(\d+)\s*.*?out\sof\s*(\d+)')
  /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:37:
SyntaxWarning: invalid escape sequence '\s'
    labelled_chi = re.compile('Chi1-chi2\splots:\s*(\d+)\s*.*?out\sof\s*(\d+)')
  /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:38:
SyntaxWarning: invalid escape sequence '\s'
    bad_contacts = re.compile('Bad\scontacts:\s*(\d+)')
  /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:39:
SyntaxWarning: invalid escape sequence '\s'
    g_factors = re.compile('G-factors\s*Dihedrals:\s*([0-9-+.]+)' +
  /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:40:
SyntaxWarning: invalid escape sequence '\s'
    '\s*Covalent:\s*([0-9-+.]+)\s*Overall:\s*([0-9-+.]+)')
  /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:32:
SyntaxWarning: invalid escape sequence '\s'
    re_ramachandran = re.compile('Ramachandran\s*Z-score\s*:\s*([0-9.Ee-]+)')
  /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:33:
SyntaxWarning: invalid escape sequence '\s'
    re_1st = re.compile('1st\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)')
  /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:34:
SyntaxWarning: invalid escape sequence '\s'
    re_2nd = re.compile('2nd\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)')
  /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:35:
SyntaxWarning: invalid escape sequence '\s'
    re_backbone =
re.compile('Backbone\s*conformation\s*Z-score\s*:\s*([0-9.Ee-]+)')
  /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:36:
SyntaxWarning: invalid escape sequence '\S'
    re_rotamer =
re.compile('chi-1\S*chi-2\s*rotamer\s*normality\s*:\s*([0-9.Ee-]+)')
  /usr/lib/python3/dist-packages/csb/bio/io/wwpdb.py:1222:
SyntaxWarning: invalid escape sequence '\d'
    res = re.search("(\d+(?:\.\d+)?)\s+ANGSTROM", line)
  /usr/lib/python3/dist-packages/csb/bio/sequence/__init__.py:566:
SyntaxWarning: invalid escape sequence '\w'
    self._residues += re.sub('([^\w\-\.])+', '', string)
  /usr/lib/python3/dist-packages/csb/bio/structure/__init__.py:2129:
SyntaxWarning: invalid escape sequence '\s'
    string = ''.join(re.split('\s+', string))
  /usr/lib/python3/dist-packages/csb/bio/structure/__init__.py:2131:
SyntaxWarning: invalid escape sequence '\s'
    conf_string = ''.join(re.split('\s+', conf_string))
  /usr/lib/python3/dist-packages/csb/statistics/__init__.py:341:
SyntaxWarning: invalid escape sequence '\s'
    """
  /usr/lib/python3/dist-packages/csb/test/cases/io/__init__.py:482:
SyntaxWarning: invalid escape sequence '\w'
    "([0-9a-zA-Z]([-.\w]*[0-9a-zA-Z])"]

Hello,

Bug #1085900 in python-csb reported by you has been fixed in the
Git repository and is awaiting an upload. You can see the commit
message below and you can check the diff of the fix at:

https://salsa.debian.org/med-team/python-csb/-/commit/54dc7d47272c95ac3b1a68d48e77b81c8f11a844

(this message was generated automatically)
-- 
Greetings

https://bugs.debian.org/1085900

We believe that the bug you reported is fixed in the latest version of
python-csb, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1085900@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated python-csb package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Fri, 23 Oct 2026 20:43:07 +0200
Source: python-csb
Architecture: source
Version: 1.2.5+dfsg-11
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Closes: 1085900 1149340
Changes:
 python-csb (1.2.5+dfsg-11) unstable; urgency=medium
 .
   * Fix Python3.12 string syntax
     Closes: #1085900
   * Exclude Python 3.15 from build (Closes: #1149340)
     as well as fixing further NumPy issues
       - replace numpy.asfarray (removed in numpy 2.0) with numpy.asarray
       - replace binary numpy.fromstring with numpy.frombuffer
       - fix failing test-suite assertions (replica exchange samplers,
         enum comparison, pickling recursion limit)
   * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
   * d/watch: version=5
   * Standards-Version: 4.7.4 (routine-update)
   * Reflow Uploaders field (cme)
   * Remove Priority field (cme)
   * Drop 'Rules-Requires-Root: no' from d/control (routine-update)
   * Reformat the Last-Update date as ISO YYYY-MM-DD.
   * debputy lint --auto-fix (routine-update)
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 4b11434539ed3a20d55c33a7fed04d636b48d1c5 14348 python-csb_1.2.5+dfsg-11.debian.tar.xz
 7d9a8fbba251d20362c0fe95c9255d7e16f35777 9228 python-csb_1.2.5+dfsg-11_amd64.buildinfo
Checksums-Sha256:
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Files:
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 ce6ae5b25d5ce80f2177af37096b4cdc 14348 science optional python-csb_1.2.5+dfsg-11.debian.tar.xz
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